Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation
Kolodziejczyk, Aleksandra A., Kim, Jong Kyoung, Tsang, Jason C.H., Ilicic, Tomislav, Henriksson, Johan, Natarajan, Kedar N., Tuck, Alex C., Gao, Xuefei +4 more·2015·Cell Stem Cell
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Items 101–200 of 578
- Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identityAlice Wenger, Alva Biran, Nicolás Alcaraz, Alba Redó Riveiro, Annika Charlotte Sell, Robert Krautz, Valentin Flury, Nazaret Reverón-Gómez, Victor Solis‐Mezarino, Moritz Carl Völker-Albert et al. · 2023 · Nature Genetics
- Genome-Scale Oscillations in DNA Methylation during Exit from PluripotencySteffen Rulands, Heather J Lee, Stephen J. Clark, Christof Angermueller, Sébastien A. Smallwood, Felix Krueger, Hisham Mohammed, Wendy Dean, Jennifer Nichols, Peter J. Rugg‐Gunn et al. · 2018 · Cell Systems
- STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cellsPeng, Tianran, Zhai, Yanan, Atlasi, Yaser, ter Huurne, Menno, Marks, Hendrik, Stunnenberg, Hendrik G., Megchelenbrink, Wout · 2020 · Genome Biology
- OCT4 Acts as an Integrator of Pluripotency and Signal-Induced DifferentiationZoltán Simándi, Attila Horváth, Lyndsey C. Wright, Ixchelt Cuaranta‐Monroy, Isabella De Luca, Katalin Károlyi, Sascha Sauer, Jean‐François Deleuze, Lorraine J. Gudas, Shaun M. Cowley et al. · 2016 · Molecular Cell
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- Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell AnalysisGuoji Guo, Luca Pinello, Xiaoping Han, Shujing Lai, Li Shen, Ta-Wei Lin, Keyong Zou, Guo‐Cheng Yuan, Stuart H. Orkin · 2016 · Cell Reports
- Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological ComplexityWilkinson, Adam C., Nakauchi, Hiromitsu, Göttgens, Berthold · 2017 · Cell Systems
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- Defining Cell Identity with Single‐Cell OmicsLaura Mincarelli, Ashleigh Lister, James Lipscombe, Iain C. Macaulay · 2018 · PROTEOMICS
- Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic backgroundSabitri Ghimire, Margot Van der Jeught, Jitesh Neupane, Matthias S. Roost, Jasper Anckaert, Mina Popovic, Filip Van Nieuwerburgh, Pieter Mestdagh, Jo Vandesompele, Dieter L. D. Deforce et al. · 2018 · Scientific Reports
- Benchmark and Parameter Sensitivity Analysis of Single-Cell RNA Sequencing Clustering MethodsMonika Krzak, Yordan P. Raykov, Alexis Boukouvalas, Luisa Cutillo, Claudia Angelini · 2019 · Frontiers in Genetics
- Single-cell RNA-seq clustering: datasets, models, and algorithmsLihong Peng, Xiongfei Tian, Geng Tian, Junlin Xu, Xin Huang, Yanbin Weng, Jialiang Yang, Liqian Zhou · 2020 · RNA Biology
- Gene length and detection bias in single cell RNA sequencing protocolsPhipson, Belinda, Zappia, Luke, Oshlack, Alicia · 2017 · F1000Research
- The Human Cell AtlasAviv Regev, Sarah Amalia Teichmann, Eric S. Lander, Ido Amit, Christophe O. Benoist, Ewan Birney, Bernd Bodenmiller, Peter J. Campbell, Piero Carninci, Menna Ruth Clatworthy et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- Valid Post-clustering Differential Analysis for Single-Cell RNA-SeqZhang, Jesse M., Kamath, Govinda M., Tse, David N. · 2019 · Cell Systems
- Critical downstream analysis steps for single-cell RNA sequencing dataZilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, Quan Zou · 2021 · Briefings in Bioinformatics
- Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomesDavis James McCarthy, Raghd Rostom, Yuanhua Huang, Daniel J. Kunz, Petr Danecek, Marc Jan Bonder, Tzachi Hagai, Ruqian Lyu, Wenyi Wang, Daniel J. Gaffney et al. · 2020 · Nature Methods
- Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degenerationAnne Senabouth, Maciej Daniszewski, Grace E. Lidgerwood, Helena Hai Liang, Damián Hernández, Mehdi Mirzaei, Stacey N. Keenan, Ran Zhang, Xikun Han, Drew R. Neavin et al. · 2022 · Nature Communications
- What has single-cell RNA-seq taught us about mammalian spermatogenesis?Shinnosuke Suzuki, Victoria D. Diaz, Brian P. Hermann · 2019 · Biology of Reproduction
- A periodic table of cell typesBo Xia, Itai Yanai · 2019 · Development
- Stable Oxidative Cytosine Modifications Accumulate in Cardiac Mesenchymal Cells From Type2 Diabetes PatientsFrancesco Spallotta, Chiara Cencioni, Sandra Atlante, Davide Garella, Mattia Cocco, Mattia Mori, Raffaella Mastrocola, Carsten Tobias Kuenne, Stefan Günther, Simona Nanni et al. · 2017 · Circulation Research
- Linking Telomere Regulation to Stem Cell PluripotencyLin Liu · 2016 · Trends in Genetics
- Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferationValentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang et al. · 2016 · Genome biology
- Activation of Lineage Regulators and Transposable Elements across a Pluripotent SpectrumJamie A. Hackett, Toshihiro Kobayashi, Sabine Dietmann, M. Azim Surani · 2017 · Stem Cell Reports
- Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9S. Ali Shariati, Antonia A. Dominguez, Shicong Xie, Marius Wernig, Lei S. Qi, Jan Marcel Skotheim · 2019 · Molecular Cell
- Global hyperactivation of enhancers stabilizes human and mouse naive pluripotency through inhibition of CDK8/19 Mediator kinasesCian J. Lynch, Raquel Bernad, Ana Martínez‐Val, Marta N. Shahbazi, Sandrina Nóbrega Pereira, Isabel Calvo, Carmen Blanco‐Aparicio, Carolina Tarantino, Elena Garreta, Laia Richart et al. · 2020 · Nature Cell Biology
- Quantitative single-cell transcriptomicsChristoph Ziegenhain, Beate Vieth, Swati Parekh, Ines Hellmann, Wolfgang Enard · 2018 · Briefings in Functional Genomics
- Single‐Cell Sequencing Methodologies: From Transcriptome to Multi‐Dimensional MeasurementYingwen Chen, Jia Tao Song, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong James Yang · 2021 · Small Methods
- All models are wrong, but some are useful: Establishing standards for stem cell-based embryo modelsEszter Pósfai, Fredrik Lanner, Carla Mulas, Harry G. Leitch · 2021 · Stem Cell Reports
- Single‐cell technologies to study the immune systemValentina Proserpio, Bidesh Mahata · 2015 · Immunology
- Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq dataWanqing Shao, Ting Wang · 2020 · Genome Research
- Sustained Trem2 stabilization accelerates microglia heterogeneity and Aβ pathology in a mouse model of Alzheimer’s diseaseDhandapani, Rahul, Neri, Marilisa, Bernhard, Mario, Brzak, Irena, Schweizer, Tatjana, Rudin, Stefan, Joller, Stefanie, Berth, Ramon, Kernen, Jasmin, Neuhaus, Anna et al. · 2022 · Cell Reports
- Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing dataAaron T. L. Lun, Fernando J. Calero‐Nieto, Liora Haim-Vilmovsky, Berthold Göttgens, John C. Marioni · 2017 · Genome Research
- Feeders facilitate telomere maintenance and chromosomal stability of embryonic stem cellsRenpeng Guo, Xiaoying Ye, Jiao Yang, Zhongcheng Zhou, Chenglei Tian, Hua Wang, Haiying Wang, Haifeng Fu, Chun Liu, Ming Zeng et al. · 2018 · Nature Communications
- Modeling signaling‐dependent pluripotency with Boolean logic to predict cell fate transitionsAyako Yachie‐Kinoshita, Kento Onishi, Joel Östblom, Matthew A. Langley, Eszter Pósfai, Janet Rossant, Peter W. Zandstra · 2018 · Molecular Systems Biology
- Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesisIsabelle Bergiers, Tallulah S. Andrews, Özge Vargel Bölükbaşı, Andreas Buneß, Ewa Janosz, Natalia López-Anguita, Kerstin Ganter, Kinga Kosim, Cemre Celen, Gülce Itır Perçin et al. · 2018 · eLife
- Single-cell transcriptional profiling: a window into embryonic cell-type specificationBlanca Pijuan-Sala, Carolina Guibentif, Berthold Göttgens · 2018 · Nature Reviews Molecular Cell Biology
- Medoid Silhouette clustering with automatic cluster number selectionLars Lenssen, Erich Schubert · 2023 · Information Systems
- Information fusion for large-scale multi-source data based on the Dempster-Shafer evidence theoryQinli Zhang, Pengfei Zhang, Tianrui Li · 2024 · Information Fusion
- scDC: single cell differential composition analysisYue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Yee Hwa Yang, Kitty Lo · 2019 · BMC Bioinformatics
- Obstacles to detecting isoforms using full-length scRNA-seq dataJennifer Westoby, Pavel Artemov, Martin Hemberg, Anne C. Ferguson‐Smith · 2020 · Genome biology
- Emerging Imaging and Genomic Tools for Developmental Systems BiologyZhe J. Liu, Philipp Keller · 2016 · Developmental Cell
- Loss of Kat2a enhances transcriptional noise and depletes acute myeloid leukemia stem-like cellsDomingues, Ana Filipa, Kulkarni, Rashmi, Giotopoulos, George, Gupta, Shikha, Vinnenberg, Laura, Arede, Liliana, Foerner, Elena, Khalili, Mitra, Adao, Rita Romano, Johns, Ayona et al. · 2020 · eLife
- An interpretable framework for clustering single-cell RNA-Seq datasetsJesse M. Zhang, Jue Fan, H. Christina Fan, David Rosenfeld, David N. C. Tse · 2018 · BMC Bioinformatics
- Single cell RNA sequencing of stem cell-derived retinal ganglion cellsMaciej Daniszewski, Anne Senabouth, Quan Hoang Nguyen, Duncan E. Crombie, Samuel W. Lukowski, Tejal Kulkarni, Valentin M. Sluch, Jafar S. Jabbari, Xitiz Chamling, Donald J. Zack et al. · 2018 · Scientific Data
- Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seqDongsheng Bai, Xiaoting Zhang, Huifen Xiang, Zijian Guo, Chenxu Zhu, Chengqi Yi · 2024 · Nature Biotechnology
- Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical OutcomesJie Wang, Shuli Xia, Brian Arand, Heng Zhu, Raghu Machiraju, Kun Huang, Hongkai Ji, Jiang X. Qian · 2016 · PLoS Computational Biology
- Consensus clustering of single-cell RNA-seq data by enhancing network affinityYaxuan Cui, Shaoqiang Zhang, Ying Jie Liang, Xiangyun Wang, Thomas N. Ferraro, Yong Chen · 2021 · Briefings in Bioinformatics
- Promoter sequence and architecture determine expression variability and confer robustness to genetic variantsHjörleifur Einarsson, Marco Salvatore, Christian Vaagensø, Nicolás Alcaraz, Jette Bornholdt, Sarah Rennie, Robin Andersson · 2022 · eLife
- Cell cycle dynamics of mouse embryonic stem cells in the ground state and during transition to formative pluripotencyAriel Waisman, Federico Sevlever, Martín Elías Costa, María Soledad Cosentino, Santiago Miriuka, Alejandra C. Ventura, Alejandra Guberman · 2019 · Scientific Reports
- Generalizable and Scalable Visualization of Single-Cell Data Using Neural NetworksHyunghoon Cho, Bonnie Berger, Jian Peng · 2018 · Cell Systems
- Random forest based similarity learning for single cell RNA sequencing dataMaziyar Baran Pouyan, Dennis Kostka · 2018 · Bioinformatics
- Integrated analysis of Xist upregulation and X-chromosome inactivation with single-cell and single-allele resolutionGuido Pacini, Ilona Dunkel, Norbert Mages, Verena Mutzel, Bernd Timmermann, Annalisa Marsico, Edda G. Schulz · 2021 · Nature Communications
- Contrasting epigenetic states of heterochromatin in the different types of mouse pluripotent stem cellsMatteo Tosolini, Vincent Brochard, Pierre G. Adenot, Martine Chebrout, Giacomo Grillo, Violette Navia, Nathalie Beaujean, Claire Francastel, Amélie Bonnet‐Garnier, Alice Jouneau · 2018 · Scientific Reports
- c-CSN: Single-Cell RNA Sequencing Data Analysis by Conditional Cell-Specific NetworkLin Li, Hao Dai, Zhaoyuan Fang, Luonan Chen · 2021 · Genomics Proteomics & Bioinformatics
- Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivationAndrea J. Kriz, David Colognori, Hongjae Sunwoo, Behnam Nabet, Jeannie T. Lee · 2021 · Molecular Cell
- Computational Tools for Stem Cell BiologyQin Bian, Patrick Cahan · 2016 · Trends in biotechnology
- IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-SeqAnjun Ma, Cankun Wang, Yuzhou Chang, Faith H. Brennan, Adam McDermaid, Bingqiang Liu, Chi Zhang, Phillip G. Popovich, Qin Ma · 2020 · Nucleic Acids Research
- A comparison of deep learning-based pre-processing and clustering approaches for single-cell RNA sequencing dataJiacheng Wang, Quan Zou, Chen Lin · 2021 · Briefings in Bioinformatics
- A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylationMeng Amy Li, Paulo Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tüzer Kalkan, Meryem Ralser, Samuel C. Robson, Ferdinand von Meyenn, Maike Paramor et al. · 2017 · eLife
- SCCLRR: A Robust Computational Method for Accurate Clustering Single Cell RNA-Seq DataWei Zhang, Yuanyuan Li, Xiufen Zou · 2020 · IEEE Journal of Biomedical and Health Informatics
- The primitive endoderm supports lineage plasticity to enable regulative developmentMadeleine Linneberg-Agerholm, Annika Charlotte Sell, Alba Redó Riveiro, Marta Perera, Martin Proks, Teresa E. Knudsen, Antonio Barral, Miguel Manzanares, Joshua M. Brickman · 2024 · Cell
- Cycling to Meet Fate: Connecting Pluripotency to the Cell CycleLamuk Zaveri, Jyotsna Dhawan · 2018 · Frontiers in Cell and Developmental Biology
- Kat6b Modulates Oct4 and Nanog Binding to Chromatin in Embryonic Stem Cells and Is Required for Efficient Neural DifferentiationMaría Soledad Cosentino, Camila Oses, Camila Vázquez Echegaray, Claudia Solari, Ariel Waisman, Yanina D. Álvarez, María Victoria Petrone, Marcos Gabriel Francia, Marcelo Schultz, Gustavo Emilio Sevlever et al. · 2019 · Journal of Molecular Biology
- Isolation and cultivation of naive-like human pluripotent stem cells based on HERVH expressionJichang Wang, Manvendra Singh, Chuanbo Sun, Daniel Besser, Alessandro Prigione, Zoltán Ivics, Laurence D. Hurst, Zsuzsanna Izsvák · 2016 · Nature Protocols
- CpG island composition differences are a source of gene expression noise indicative of promoter responsivenessMichael David Morgan, John C. Marioni · 2018 · Genome biology
- Simulation-based benchmarking of isoform quantification in single-cell RNA-seqJennifer Westoby, Marcela K. Sjöberg-Herrera, Anne C. Ferguson‐Smith, Martin Hemberg · 2018 · Genome biology
- Single-Cell Clustering Based on Shared Nearest Neighbor and Graph PartitioningXiaoshu Zhu, Jie Zhang, Yunpei Xu, Jianxin Wang, Xiaoqing Peng, Hong‐Dong Li · 2020 · Interdisciplinary Sciences Computational Life Sciences
- NMFLRR: Clustering scRNA-Seq Data by Integrating Nonnegative Matrix Factorization With Low Rank RepresentationWei Zhang, Xiaoli Xue, Xiaoying Zheng, Zizhu Fan · 2021 · IEEE Journal of Biomedical and Health Informatics
- Esrrb guides naive pluripotent cells through the formative transcriptional programmeElena Carbognin, Valentina Carlini, Francesco Panariello, Martina Chieregato, Elena Guerzoni, Davide Benvegnù, Valentina Perrera, Cristina Malucelli, Marcella Cesana, Antonio Grimaldi et al. · 2023 · Nature Cell Biology
- Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate TransitionsLi Sun, Xiuling Fu, Gang Ma, Andrew P. Hutchins · 2021 · Frontiers in Cell and Developmental Biology
- Live birth of chimeric monkey with high contribution from embryonic stem cellsJing Cao, Wenjuan Li, Jie Li, Md. Abdul Mazid, Chunyang Li, Yu Jiang, Wenqi Jia, Liang Li Wu, Zhaodi Liao, Shiyu Sun et al. · 2023 · Cell
- Stem Cell Impairment at the Host-Microbiota Interface in Colorectal CancerMarinella Marzano, Bruno Fosso, Elisabetta Piancone, Giuseppe Defazio, Graziano Pesole, Mariangela De Robertis · 2021 · Cancers
- The combined action of Esrrb and Nr5a2 is essential for murine naïve pluripotencyNicola Festuccia, Nick D. L. Owens, Almira A. Chervova, Agnès Dubois, Pablo Navarro · 2021 · Development
- Stat3 activation is critical for pluripotency maintenanceYan Zhang, Dan Wang, Jia Xu, Yuebing Wang, Fengxia Ma, Zongjin Li, Na Liu · 2018 · Journal of Cellular Physiology
- Kaposi's Sarcoma-Associated Herpesvirus Hijacks RNA Polymerase II To Create a Viral Transcriptional FactoryChristopher Phillip Chen, Yuanzhi Lyu, Frank Y.S. Chuang, Kazushi Nakano, Chie Izumiya, Di Jin, Mel Campbell, Yoshihiro Izumiya · 2017 · Journal of Virology
- SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-Scale Single Cell RNA-Seq DataXianwen Ren, Liangtao Zheng, Zemin Zhang · 2019 · Genomics Proteomics & Bioinformatics
- Retinal ganglion cell-specific genetic regulation in primary open-angle glaucomaMaciej Daniszewski, Anne Senabouth, Helena Hai Liang, Xikun Han, Grace E. Lidgerwood, Damián Hernández, Priyadharshini Sivakumaran, Jordan Elli Clarke, Shiang Yong Lim, Jarmon G. Lees et al. · 2022 · Cell Genomics
- Single-cell analysis reveals lineage segregation in early post-implantation mouse embryosJing Wen, Yanwu Zeng, Zhuoqing Fang, Junjie Gu, Laixiang Ge, Fan Tang, Zepeng Qu, Jing Hu, Yaru Cui, Kushan Zhang et al. · 2017 · Journal of Biological Chemistry
- Distinctive features of lincRNA gene expression suggest widespread RNA-independent functionsAlex Tuck, Kedar Nath Natarajan, Greggory M. Rice, Jason A. Borawski, Fabio Mohn, Aneliya Rankova, Matyáš Flemr, Alice Wenger, Razvan Nutiu, Sarah Amalia Teichmann et al. · 2018 · Life Science Alliance
- Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary StudiesElisa Buchberger, Micael Reis, Ting-Hsuan Lu, Nico Posnien · 2019 · Genes
- The impact of microRNAs on transcriptional heterogeneity and gene co-expression across single embryonic stem cellsGennaro Gambardella, Annamaria Carissimo, Amy F. Chen, Luisa Cutillo, Tomasz Jan Nowakowski, Diego di Bernardo, Robert H. Blelloch · 2017 · Nature Communications
- Fast identification of differential distributions in single-cell RNA-sequencing data with waddRRoman Schefzik, Julian Flesch, Ângela Gonçalves · 2021 · Bioinformatics
- A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis BullosaHuanan Zhang, Catherine A. A. Lee, Zhuliu Li, John Garbe, Cindy R. Eide, Raphael Petegrosso, Rui Kuang, Jakub Tolar · 2018 · PLoS Computational Biology
- Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding TranscriptsIsaac A. Babarinde, Yuhao Li, Andrew P. Hutchins · 2019 · Computational and Structural Biotechnology Journal
- Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cellsMarcel Tarbier, Sebastian D. Mackowiak, João Frade, Silvina Catuara‐Solarz, Inna Biryukova, Eleni Gelali, Diego Bárcena Menéndez, Luis Zapata, Stephan Ossowski, Magda Bienko et al. · 2020 · Nature Communications
- Polyploidy and Myc Proto-Oncogenes Promote Stress Adaptation via Epigenetic Plasticity and Gene Regulatory Network RewiringO. V. Anatskaya, A. Vinogradov · 2022 · International Journal of Molecular Sciences
- Critical Role for P53 in Regulating the Cell Cycle of Ground State Embryonic Stem CellsMenno ter Huurne, Tianran Peng, Guoqiang Yi, Guido van Mierlo, Hendrik Marks, Hendrik G. Stunnenberg · 2020 · Stem Cell Reports
- Global and targeted approaches to single-cell transcriptome characterizationAleksandra A. Kolodziejczyk, Tapio Lönnberg · 2017 · Briefings in Functional Genomics
- Systems-Wide Approaches in Induced Pluripotent Stem Cell ModelsEdward Lau, David T. Paik, Joseph C. Wu · 2018 · Annual Review of Pathology Mechanisms of Disease
- Nanog induced intermediate state in regulating stem cell differentiation and reprogrammingPeijia Yu, Qing Hua Nie, Chao Tang, Lei Zhang · 2018 · BMC Systems Biology
- Learning regulatory models for cell development from single cell transcriptomic dataAnn C. Babtie, Thalia E. Chan, Michael P.H. Stumpf · 2017 · Current Opinion in Systems Biology
- An empirical comparison and characterisation of nine popular clustering methodsChristian Martin Hennig · 2022 · Advances in Data Analysis and Classification
- Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoderJing Jiang, Junlin Xu, Yuansheng Liu, Bosheng Song, Xiulan Guo, Xiangxiang Zeng, Quan Zou · 2023 · Briefings in Bioinformatics
- Modeling Mammalian Commitment to the Neural Lineage Using Embryos and Embryonic Stem CellsRachel A. Shparberg, Hannah J. Glover, Michael B. Morris · 2019 · Frontiers in Physiology
- Emerging deep learning methods for single‐cell RNA‐seq data analysisJie Zheng, Ke Wang · 2019 · Quantitative Biology
- Cell competition and the regulative nature of early mammalian developmentJennifer Nichols, Ana Lima, Tristan A. Rodríguez · 2022 · Cell stem cell
- Falco: a quick and flexible single-cell RNA-seq processing framework on the cloudAndrian Yang, Michael Troup, Peijie Lin, Joshua W. K. Ho · 2016 · Bioinformatics
- Dissection of two routes to naïve pluripotency using different kinase inhibitorsAna Martínez‐Val, Cian J. Lynch, Isabel Calvo, Pilar Ximénez‐Embún, Fernando Garcı́a, Eduardo Zarzuela, Manuel Serrano, Javier Muñoz · 2021 · Nature Communications
- SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq dataYushan Qiu, Yan Chang, Pu Zhao, Quan Zou · 2023 · Briefings in Bioinformatics